From 0a8ad6bd938bc31797e71ea04bbb13e05b2fb3a3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Nov 2022 11:50:04 +0100 Subject: [PATCH 1/8] update gatk4/haplotypecaller --- modules.json | 392 ++++++++++++++---- modules/nf-core/gatk4/haplotypecaller/main.nf | 9 +- .../nf-core/gatk4/haplotypecaller/meta.yml | 4 + 3 files changed, 326 insertions(+), 79 deletions(-) diff --git a/modules.json b/modules.json index 001413f95f..32704ff61c 100644 --- a/modules.json +++ b/modules.json @@ -7,327 +7,567 @@ "nf-core": { "ascat": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", - "git_sha": "78cf39939fbe160a1410c44a6c5946f9a4c56e7e" + "git_sha": "78cf39939fbe160a1410c44a6c5946f9a4c56e7e", + "installed_by": [ + "modules" + ] }, "bcftools/stats": { "branch": "master", - "git_sha": "78cf39939fbe160a1410c44a6c5946f9a4c56e7e" + "git_sha": "78cf39939fbe160a1410c44a6c5946f9a4c56e7e", + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", - "git_sha": "9518fa4f65f3fb8cde24fde7d40333b39ec8fd65" + "git_sha": "9518fa4f65f3fb8cde24fde7d40333b39ec8fd65", + "installed_by": [ + "modules" + ] }, "bwa/mem": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01" + "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "installed_by": [ + "modules" + ] }, "bwamem2/index": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": [ + "modules" + ] }, "bwamem2/mem": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01" + "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": [ + "modules" + ] }, "cnvkit/antitarget": { "branch": "master", - 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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": [ + "modules" + ] }, "vcftools": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": [ + "modules" + ] } } } diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 9347fbbc10..51572176df 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -16,9 +16,10 @@ process GATK4_HAPLOTYPECALLER { path dbsnp_tbi output: - tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val(meta), path("*.tbi") , optional:true, emit: tbi - path "versions.yml" , emit: versions + tuple val(meta), path("*.vcf.gz") , emit: vcf + tuple val(meta), path("*.tbi") , optional:true, emit: tbi + tuple val(meta), path("*.realigned.bam"), optional:true, emit: bam + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -29,6 +30,7 @@ process GATK4_HAPLOTYPECALLER { def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : "" def interval_command = intervals ? "--intervals $intervals" : "" def dragstr_command = dragstr_model ? "--dragstr-params-path $dragstr_model" : "" + def bamout_command = args.contains("--bam-writer-type") ? "--bam-output ${prefix.replaceAll('.g\\s*$', '')}.realigned.bam" : "" def avail_mem = 3 if (!task.memory) { @@ -44,6 +46,7 @@ process GATK4_HAPLOTYPECALLER { $dbsnp_command \\ $interval_command \\ $dragstr_command \\ + $bamout_command \\ --tmp-dir . \\ $args diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml index 48193d91f3..cef608b4a2 100644 --- a/modules/nf-core/gatk4/haplotypecaller/meta.yml +++ b/modules/nf-core/gatk4/haplotypecaller/meta.yml @@ -73,6 +73,10 @@ output: type: file description: Index of VCF file pattern: "*.vcf.gz.tbi" + - bam: + type: file + description: Assembled haplotypes and locally realigned reads + pattern: "*.realigned.bam" authors: - "@suzannejin" From 59f5fdd554eb11563ab6dd396a22905de6753fa1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Nov 2022 11:58:52 +0100 Subject: [PATCH 2/8] gather realigned bams --- .../main.nf | 30 +++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf b/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf index bdd518e9d1..8114d37d4d 100644 --- a/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf +++ b/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf @@ -1,7 +1,8 @@ -include { GATK4_MERGEVCFS as MERGE_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/mergevcfs/main' -include { GATK4_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/haplotypecaller/main' include { BAM_JOINT_CALLING_GERMLINE_GATK } from '../bam_joint_calling_germline_gatk/main' +include { BAM_MERGE_INDEX_SAMTOOLS } from '../bam_merge_index_samtools/main' include { VCF_VARIANT_FILTERING_GATK } from '../vcf_variant_filtering_gatk/main' +include { GATK4_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/haplotypecaller/main' +include { GATK4_MERGEVCFS as MERGE_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/mergevcfs/main' workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER { take: @@ -42,6 +43,11 @@ workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER { no_intervals: it[0].num_intervals <= 1 }.set{haplotypecaller_tbi_branch} + GATK4_HAPLOTYPECALLER.out.bam.branch{ + intervals: it[0].num_intervals > 1 + no_intervals: it[0].num_intervals <= 1 + }.set{haplotypecaller_bam_branch} + if (params.joint_germline) { // merge vcf and tbis genotype_gvcf_to_call = Channel.empty().mix(GATK4_HAPLOTYPECALLER.out.vcf @@ -100,6 +106,25 @@ workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER { MERGE_HAPLOTYPECALLER.out.tbi, haplotypecaller_tbi_branch.no_intervals) + // BAM output + BAM_MERGE_INDEX_SAMTOOLS( + haplotypecaller_bam_branch.intervals + .map{ meta, bam -> + + new_meta = [ + id: meta.sample, + num_intervals: meta.num_intervals, + patient: meta.patient, + sample: meta.sample, + sex: meta.sex, + status: meta.status + ] + + [groupKey(new_meta, new_meta.num_intervals), bam] + }.groupTuple().mix(haplotypecaller_bam_branch.no_intervals)) + + realigned_bam = BAM_MERGE_INDEX_SAMTOOLS.out.bam_bai + VCF_VARIANT_FILTERING_GATK(haplotypecaller_vcf.join(haplotypecaller_tbi), fasta, fasta_fai, @@ -117,4 +142,5 @@ workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER { emit: versions = ch_versions filtered_vcf + realigned_bam } From 83701c292b7a111621bd8ed4ae351aea0b8372ae Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 24 Nov 2022 11:00:36 +0000 Subject: [PATCH 3/8] [automated] Fix linting with Prettier --- modules.json | 320 +++++++++++++-------------------------------------- 1 file changed, 80 insertions(+), 240 deletions(-) diff --git a/modules.json b/modules.json index 32704ff61c..8db91548ae 100644 --- a/modules.json +++ b/modules.json @@ -8,566 +8,406 @@ "ascat": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - 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"modules" - ] + "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/view": { "branch": "master", "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "snpeff": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "strelka/germline": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "strelka/somatic": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiddit/sv": { "branch": "master", "git_sha": "89f98091ac9e1653657b9e324e394b158d723a4f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "unzip": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcftools": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } } From 7d31f4f46d292cae845402fd89eac92784296a67 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Nov 2022 12:06:54 +0100 Subject: [PATCH 4/8] fix merge conflicts --- modules.json | 2 -- 1 file changed, 2 deletions(-) diff --git a/modules.json b/modules.json index b347aef273..5e3473a5c9 100644 --- a/modules.json +++ b/modules.json @@ -367,7 +367,6 @@ "snpeff": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": ["modules"] "installed_by": ["modules", "vcf_annotate_snpeff"] }, "strelka/germline": { @@ -388,7 +387,6 @@ "tabix/bgziptabix": { "branch": "master", "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": ["modules"] "installed_by": ["modules", "vcf_annotate_snpeff"] }, "tabix/tabix": { From 80ea7cd40791cb868b7770eb0394ead5a0d3c51d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Nov 2022 13:11:07 +0100 Subject: [PATCH 5/8] add publish directives for the bam files --- conf/modules/haplotypecaller.config | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/conf/modules/haplotypecaller.config b/conf/modules/haplotypecaller.config index 1d5536785d..5f5d7501de 100644 --- a/conf/modules/haplotypecaller.config +++ b/conf/modules/haplotypecaller.config @@ -118,4 +118,16 @@ process { pattern: "*{vcf.gz,vcf.gz.tbi}" ] } + + if (!(params.tools && params.tools.split(',').contains('haplotypecaller'))) { + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)' { + ext.prefix = { "${meta.id}.realigned" } + publishDir = [ + enabled: true, + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/" }, + pattern: "*{bam,bai}" + ] + } + } } From 0ecea5cc25350727fc350c485ea50a920d8706e8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Nov 2022 13:15:20 +0100 Subject: [PATCH 6/8] update test tags --- tests/config/pytest_tags.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/config/pytest_tags.yml b/tests/config/pytest_tags.yml index f16bb5a699..d2440f6c77 100644 --- a/tests/config/pytest_tags.yml +++ b/tests/config/pytest_tags.yml @@ -164,8 +164,11 @@ haplotypecaller: - modules/nf-core/gatk4/haplotypecaller/main.nf - modules/nf-core/gatk4/mergevcfs/main.nf - modules/nf-core/gatk4/variantrecalibrator/main.nf + - modules/nf-core/samtools/index/main.nf + - modules/nf-core/samtools/merge/main.nf - modules/nf-core/tabix/tabix/main.nf - subworkflows/local/bam_joint_calling_germline_gatk/main.nf + - subworkflows/local/bam_merge_index_samtools/main.nf - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf - subworkflows/local/vcf_variant_filtering_gatk/main.nf From 5c6017a6c398bf9d1c30a1046271c7e48208a577 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Nov 2022 14:48:49 +0100 Subject: [PATCH 7/8] fix non-existing channel when joint germline variant calling --- subworkflows/local/bam_variant_calling_haplotypecaller/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf b/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf index 8114d37d4d..ebf13d2d47 100644 --- a/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf +++ b/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf @@ -23,6 +23,7 @@ workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER { ch_versions = Channel.empty() filtered_vcf = Channel.empty() + realigned_bam = Channel.empty() GATK4_HAPLOTYPECALLER( cram, From 16ac8f69eb57c36a2b01a71a0fb990cf5d4c8cff Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Nov 2022 15:26:18 +0100 Subject: [PATCH 8/8] update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 38d9117470..5ab7ae1f17 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- [#864](https://github.com/nf-core/sarek/pull/864) - Added possibilities to export assembled haplotypes and locally realigned reads + ### Changed - [#859](https://github.com/nf-core/sarek/pull/859) - Back to dev